Physical properties molecular dynamics

PHYSICAL PROPERTIES MOLECULAR DYNAMICS, DIFFUSION, TRANS-BILAYER TRANSLOCATION, AND LIPID EXCHANGE IN BILAYERS... 

To end this section and the review, we mention briefly the first results from the simulation on laboratory-frame cross-correlation of the type (v(f)J (0)). Here v is the molecular center-of-mass linear velocity and J is the molecular angular momentum in the usual laboratory frame of reference. For chiral molecules the center-of-mass linear velocity v seems to be correlated directly in the laboratory frame with the molecule s own angular momentum J at different points r in the time evolution of the molectilar ensemble. This is true in both the presence and absence of an external electric field. These results illustrate the first direct observation of elements of (v(r)J (0)) in the laboratory frame of reference. The racemic modification of physical and molecular dynamical properties depends, therefore, on the theorem (v(r)J (0)) 0 in both static and moving frames of reference. An external electric field enhances considerably the magnitude of the cross-correlations. 

The dynamic behaviour of polymer molecules is the bridging element in understanding the relationship between the chemical structure of a polymer and its physical properties. Molecular movement usually involves some change in the conformation of parts of the polymer chain. Since many readers may not have had experience of conformational analysis, it is now appropriate to consider the various forms of motion which are possible for polymers by starting with their small molecule analogues. 

Clusters are intennediates bridging the properties of the atoms and the bulk. They can be viewed as novel molecules, but different from ordinary molecules, in that they can have various compositions and multiple shapes. Bare clusters are usually quite reactive and unstable against aggregation and have to be studied in vacuum or inert matrices. Interest in clusters comes from a wide range of fields. Clusters are used as models to investigate surface and bulk properties [2]. Since most catalysts are dispersed metal particles [3], isolated clusters provide ideal systems to understand catalytic mechanisms. The versatility of their shapes and compositions make clusters novel molecular systems to extend our concept of chemical bonding, stmcture and dynamics. Stable clusters or passivated clusters can be used as building blocks for new materials or new electronic devices [4] and this aspect has now led to a whole new direction of research into nanoparticles and quantum dots (see chapter C2.17). As the size of electronic devices approaches ever smaller dimensions [5], the new chemical and physical properties of clusters will be relevant to the future of the electronics industry. 

Allara D L and Nuzzo R G 1985 Spontaneously organized molecular assemblies. 1. Formation, dynamics, and physical-properties of normal-alkanoic acids adsorbed from solution on an oxidized aluminum surface Langmuir 1 45-52... 

Verlet, L. Computer Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules. Physical Review 159 (1967) 98-103 Janezic, D., Merzel, F. Split Integration Symplectic Method for Molecular Dynamics Integration. J. Chem. Inf. Comput. Sci. 37 (1997) 1048-1054 McLachlan, R. I. On the Numerical Integration of Ordinary Differential Equations by Symplectic Composition Methods. SIAM J. Sci. Comput. 16 (1995) 151-168... 

The explicit definition of water molecules seems to be the best way to represent the bulk properties of the solvent correctly. If only a thin layer of explicitly defined solvent molecules is used (due to hmited computational resources), difficulties may rise to reproduce the bulk behavior of water, especially near the border with the vacuum. Even with the definition of a full solvent environment the results depend on the model used for this purpose. In the relative simple case of TIP3P and SPC, which are widely and successfully used, the atoms of the water molecule have fixed charges and fixed relative orientation. Even without internal motions and the charge polarization ability, TIP3P reproduces the bulk properties of water quite well. For a further discussion of other available solvent models, readers are referred to Chapter VII, Section 1.3.2 of the Handbook. Unfortunately, the more sophisticated the water models are (to reproduce the physical properties and thermodynamics of this outstanding solvent correctly), the more impractical they are for being used within molecular dynamics simulations. 

One drawback to a molecular dynamics simulation is that the trajectory length calculated in a reasonable time is several orders of magnitude shorter than any chemical process and most physical processes, which occur in nanoseconds or longer. This allows yon to study properties that change w ithin shorter time periods (such as energy finctnations and atomic positions), but not long-term processes like protein folding. 

In Chapter 2, a brief discussion of statistical mechanics was presented. Statistical mechanics provides, in theory, a means for determining physical properties that are associated with not one molecule at one geometry, but rather, a macroscopic sample of the bulk liquid, solid, and so on. This is the net result of the properties of many molecules in many conformations, energy states, and the like. In practice, the difficult part of this process is not the statistical mechanics, but obtaining all the information about possible energy levels, conformations, and so on. Molecular dynamics (MD) and Monte Carlo (MC) simulations are two methods for obtaining this information... 

Molecular dynamics simulation, which provides the methodology for detailed microscopical modeling on the atomic scale, is a powerful and widely used tool in chemistry, physics, and materials science. This technique is a scheme for the study of the natural time evolution of the system that allows prediction of the static and dynamic properties of substances directly from the underlying interactions between the molecules. 

A more practical approach for larger systems is molecular dynamics. In this method, the properties of bonds are determined through a combination of quantum-mechanical simulation and physical experiments, and stored in a database called a (semi-empirical) force field. Then a classical (non-quantum) simulation is done where bonds are modeled as spring-like interactions. Molecular... 

Better physical properties due to molecular regularity (esp. dynamic properties, high-performance elastomers)... 

Chui, Y.H., Grodiola, G., Snook, l.K. and Russo, S.P. (2007) Molecular dynamics investigation of the structural and thermodynamic properties of gold nanodusters of different morphologies. Physical Review B - Condensed Matter, 75, 033404-1-033404-4. 

KirchhofF, F., Mehl, M.J., Papanicolaou, N.I., Papaconstantopoulos, D.A. and Khan, F.S. (2001) Dynamical properties of Au from tight-binding molecular-dynamics simulations. Physical Review B -Condensed Matter, 63,195101-1-195101-7. 

Oral bioavailability of a drug is primarily dependent upon its rate and extent of drug absorption and systemic clearance. Systemic clearance is primarily composed of hepatic, renal and biliary clearance. The PK properties are in turn directly impacted by the drug s physical properties, such as, log P, log D and pKa. The physical properties are in turn a function of the compound s structure, molecular weight, number of hydrogen bond donors and acceptors, and number of rotatable bonds. Oral bioavailability is the outcome from the dynamic interplay of these factors in the biological system. 

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